Re: [ccp4bb] Meaning of a pdb entry

[Gergely Katona]

Dear Marcin,

Thank you for these examples! It is reassuring to see that multiple 
crystallographic models do not break validation for example. I assume only the 
validation of the first model and first reflection file is shown. I can imagine 
that it is still a substantial change and may require an extended description 
to make such depositions fully functional. I will ask the PDB, but this made me 
optimistic. It would be easy to implement Tim's method if it works for 
deposition.

Best wishes,

Gergely

-Original Message-
From: Marcin Wojdyr  
Sent: den 1 juni 2021 21:23
To: Gergely Katona 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Meaning of a pdb entry

Dear Gergely,

For authoritative advice you'd need to ask the PDB. Below is my take.

> I am not sure if it is possible to use MODEL-ENDMDL loops in pdb or mmcif 
> format for storing multiple crystallographic models.

It's possible, there are a few examples such as 2VTU. They represent "ensemble 
refinement" of a crystal structure. So it's one refinement of one dataset, but 
with multiple models.

> I assume it is already possible to store multiple structure factor files (for 
> refinement, for phasing, different crystals etc) under the same entry.

yes

> In my mind, it would be a small step to associate different data sets 
> distinguished by crystal ID or data block with a particular model number, but 
> maybe it is not that simple.
>

It'd be a substantial change, but indeed, the changes in the file format would 
not be that big. As you wrote, model IDs would need to be associated with 
crystal IDs. And probably other associations would be needed, such as unit cell 
with crystal.

> I do not want to create multiple pdb entries just to provide evidence for the 
> robustness/reproducibility of crystals and crystallographic models. I would 
> rather use different pdb entries for different sampling intentions: for 
> example entry 1 contains all the control crystals, entry 2 contains all the 
> crystals subjected to treatment A, etc.

I think it's similar to PanDDA depositions, but I don't know what's the current 
best practice.
Initially, one Deposition Group would have hundreds of PDB entries (each with a 
single dataset). But later on I've seen entries with a single model and 
hundreds of datasets. I haven't looked into it closely, so perhaps someone else 
can advise.

Concatenating multiple mmCIF files (with coordinates) would produce a 
syntactically valid file, but I don't think that such file would get through 
the deposition process.

Marcin



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Re: [ccp4bb] Meaning of a pdb entry

[Gergely Katona]

Dear Ethan,

This is an interesting discussion. I agree the word uncertainty covers very 
broad concepts, but I try to narrow down what I mean. 
My starting point is that a reflection file contains point estimates of 
diffraction intensities or structure factor amplitudes. Refinement and model 
building results in a point estimate of a structural model. These estimates can 
be calculated to arbitrary precision. The variation in these parameters are 
expected from sampling. Sampling of experimental data and sampling of 
(pseudo)random events in refinement and model building algorithms. I ignore the 
role of human influence and bias for now. Error models with different 
assumptions may help to quantify the expected variation, but if I want to 
verify these error models or just have an alternative way of quantifying 
uncertainty I have to go back to sampling. 

1) This is definitely the mean position for this atom in this crystal but there 
is uncertainty in how much individual instances in different crystal unit cells 
within the lattice deviate from this mean.

Ultimately, this is the category "unknown" for me, I cannot narrow down the 
atomic positions towards a single point with just sampling or with any of the 
experimental methods that I am aware of. The best I can achieve is to improve 
the accuracy and precisions of the model parameters of the distribution that 
describe the distributions of atomic positions.

2) This is a best-effort description of the position of a ligand atom.  However 
it is uncertain what fraction of the unit cells contain the ligand at this 
position, or at all.

My uncertainty is tied to my model, but I can chose different models of course. 
I cannot tell the fraction of unit cells containing the ligand if it is not 
part of my model and I cannot estimate the uncertainty of this parameter by 
sampling. Should I face such question, I might try to compare the average 
B-factors of the ligand that is part of my model in from different samples and 
compare it to a set of control measurements. The control model should also 
contain parameters for the ligand otherwise I cannot perform a comparison. 
Clearly, this could be misinterpreted by someone else as a determined location 
of the ligand in the control group, because the crystallographic models in the 
PDB traditionally do not represent a tool for asking questions, but the best 
effort determination of the "true" structure or ensemble. 

I could define a dependent model parameter which integrates the omit electron 
density in a certain region of the ASU and I can compare the control and soaked 
group of crystals. This is a dependent/deterministic parameter, because its 
variation will entirely depend on the variation of reflection data and the 
variation of not omitted atom positions/parameters. These type of deterministic 
model parameters are not traditionally part of a crystallographic model in a 
PDB entry. Again, this could be misinterpreted as a lack of ligand atoms/lack 
of ligand in the treated group.
  
The purpose of a PDB entry evolved over time from a single type of 
crystallographic model to include, multiple NMR models, different models, 
different methods, experimental data, validation etc. I expect that this nearly 
imperceptible evolution will continue in different directions at different 
speeds. If what I try to achieve now deviates from the current perception of 
the purpose of a PDB entry then of course I have to find other means to fulfill 
my obligation to make my data open to access. Fortunately, the data I plan to 
archive is not related to the determination of ligand occupancy and perhaps 
more in line with the current purpose of the PDB.

3) It is likely that this sidechain/loop/subunit is present in different 
conformations in different copies of the unit cell.

This is again the unknown category that I cannot address by sampling. The model 
can be open to grow (non-parametric), if the refinement is coupled to automated 
rebuilding. I have to define my question differently, for example ask how many 
conformations or water molecules were built in the control and treated group. 
Interpretation may vary, but I may have sufficient evidence of significantly 
different models in the different groups.

If the variation is better represented in pdb entries, machine learning 
algorithms can also achieve better predictions, less biased towards an 
arbitrary model sample.

4) The coordinates of this specific atom/residue/conformation are well 
supported by the data for this particular crystal.
But it might be somewhere else in the next crystal from the same 
crystallization drop, or in a crystal from a different crystallization buffer, 
or at another temperature, or in solution, or in the presence of a ligand, etc.

I am interested in representing the type of variation I cannot control and when 
designing the experiment it is in my best interest to limit the variation of 
experimental conditions between the sampl

[ccp4bb] postdoc fellowship in cryo-EM of virus replication, deadline 9 July

[Lars-Anders Carlson]

Dear colleagues,
There’s an open postdoc fellowship in my group at Umeå University, 
Sweden. The postdoc will use biochemistry and cryo-EM to study RNA virus 
replication. But don’t worry, it’s not *that* RNA virus so the 
successful candidate will be entitled to perks such as regular sleep and 
enjoying the great outdoors of northern Sweden.


We are located in the same building as Umeå Centre for Electron 
Microscopy where the postdoc will have ample access to all cryo-EM 
hardware they may desire (Krios, Scios, CLEM, fully equipped sample prep 
lab, etc). As importantly, the project is part of a collaborative 
environment between four labs that together have expertise on the full 
range from protein to organism level, including e.g. BSL3 virology work 
and advanced light microscopy. There is thus plenty of opportunity to 
expand the project in different directions.


At the core of the project is biochemistry and structural biology, so an 
ideal candidate would have prior experience in those fields. 
Specifically, we can offer training in cryo-EM to a candidate with a 
strong background in e.g. biochemistry and other structural methods. 
Highly motivated candidates with alternative backgrounds are also 
encouraged to apply.


Deadline 9 July. Contact me in case of any questions.

info about the lab:
http://www.carlsonlab.se/

more details about the application e.g. here:
https://www.researchgate.net/job/952880_Postdoc_fellowship_in_cryo-EM_structural_studies_of_RNA_virus_replication

Best wishes,
Lars



--
Lars-Anders Carlson
Assistant Professor
Dept of Medical Biochemistry and Biophysics
Wallenberg Centre for Molecular Medicine
Molecular Infection Medicine Sweden
Umeå University
901 87 Umeå, Sweden
http://www.carlsonlab.se/



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[ccp4bb] PhD position in Structural Biology, University of Münster

[Kümmel , Daniel]

Our group at the Institute of Biochemistry, University of Münster, is seeking 
to fill the position of a PhD student. This fixed-term DFG-funded post is 
available immediately for a 3 year period.



We are interested in molecular mechanisms of regulatory protein complexes in 
intracellular transport and signaling. We are looking for motivated candidates 
with a background in biochemistry and/or structural biology to continue our 
work on the molecular function of the TSC (tuberous sclerosis complex) tumor 
suppressor complex.



Working on this project will include crystallographic and electron microscopy 
studies for protein structure determination supported by biophysical, 
biochemical and cell biological experiments.

For more information, please see our recent publications (Zech et al., J Biol 
Chem 2016; Hansmann et al., Structure 2020; Fitzian et al., Mol Cell 2021) or 
visit: 
www.uni-muenster.de/Chemie.bc/research/DK/bc-research-DK-intro.html



Official job posting:

www.uni-muenster.de/Rektorat/Stellen/ausschreibungen/st_20211705_sk1.html



Please submit your inquiries and application with the usual documents by e-mail 
until 18.06.2021 to:

Prof. Dr. Daniel Kümmel

Institute of Biochemistry

Corrensstraße 36

48149 Münster
Email: daniel.kuem...@wwu.de



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[ccp4bb] superpose crystal objects in CCP4MG or other software

[Stefano Trapani]

 

Dear all 

I would like to visually compare (using some molecular graphics
software) the crystal packing of two different crystal forms of the same
protein. 

In order to identify the similarities/differences between the crystal
packings, I need to change the default unit cell origin and orientation
of one of the crystal forms. 

* Is there a way, in CCP4MG or other molecular graphics software, to
apply a given rotation/translation matrix to a "crystal object" (not to
a single molecular object), so that further expansions of the object by
crystal symmetry will be consistent with the new origin/orientation ?

* If yes: can the transformation be defined by a least-squares
superposition between molecules from the two crystal objects ?

Best regards 

-- 
Stefano Trapani

Maître de Conférences
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
-
Centre de Biologie Structurale (CBS)
29 rue de Navacelles
34090 MONTPELLIER Cedex, France

Tel : +33 (0)4 67 41 77 29
Fax : +33 (0)4 67 41 79 13
-
Université de Montpellier
CNRS UMR 5048
INSERM UMR 1054
-

 
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[ccp4bb] AW: [ccp4bb] superpose crystal objects in CCP4MG or other software

[Schreuder, Herman /DE]

Dear Stefano,
I do not know if it is possible, but as a workaround, you could first expand 
your object by crystallographic symmetry and then do the superposition.
Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von Stefano Trapani
Gesendet: Mittwoch, 2. Juni 2021 14:31
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] superpose crystal objects in CCP4MG or other software


Dear all

I would like to visually compare (using some molecular graphics software) the 
crystal packing of two different crystal forms of the same protein.

In order to identify the similarities/differences between the crystal packings, 
I need to change the default unit cell origin and orientation of one of the 
crystal forms.

  *   Is there a way, in CCP4MG or other molecular graphics software, to apply 
a given rotation/translation matrix to a "crystal object" (not to a single 
molecular object), so that further expansions of the object by  crystal 
symmetry will be consistent with the new origin/orientation ?

  *   If yes: can the transformation be defined by a least-squares 
superposition between molecules from the two crystal objects ?

Best regards

--
Stefano Trapani



Maître de Conférences

http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani

-

Centre de Biologie Structurale (CBS)

29 rue de Navacelles

34090 MONTPELLIER Cedex, France



Tel : +33 (0)4 67 41 77 29

Fax : +33 (0)4 67 41 79 13

-

Université de Montpellier

CNRS UMR 5048

INSERM UMR 1054

-

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Re: [ccp4bb] {Disarmed} AW: [ccp4bb] superpose crystal objects in CCP4MG or other software

[Stefano Trapani]

 

Yes, that is the way I usually do, but it can be cumbersome. 

It would be easier if I could first superpose two molecules from the two
crystals, and then decide in which directions to expand by crystal
symmetry (I want to compare layers and rows of molecules). 

Best regards 

Stefano 

Le 2021-06-02 15:05, Schreuder, Herman /DE a écrit : 

> Dear Stefano, 
> 
> I do not know if it is possible, but as a workaround, you could first expand 
> your object by crystallographic symmetry and then do the superposition. 
> 
> Best, 
> 
> Herman 
> 
> VON: CCP4 bulletin board  IM AUFTRAG VON Stefano 
> Trapani
> GESENDET: Mittwoch, 2. Juni 2021 14:31
> AN: CCP4BB@JISCMAIL.AC.UK
> BETREFF: [ccp4bb] superpose crystal objects in CCP4MG or other software 
> 
> Dear all 
> 
> I would like to visually compare (using some molecular graphics software) the 
> crystal packing of two different crystal forms of the same protein. 
> 
> In order to identify the similarities/differences between the crystal 
> packings, I need to change the default unit cell origin and orientation of 
> one of the crystal forms. 
> 
> * Is there a way, in CCP4MG or other molecular graphics software, to apply a 
> given rotation/translation matrix to a "crystal object" (not to a single 
> molecular object), so that further expansions of the object by crystal 
> symmetry will be consistent with the new origin/orientation ?
> 
> * If yes: can the transformation be defined by a least-squares superposition 
> between molecules from the two crystal objects ?
> 
> Best regards 
> 
> -- 
> Stefano Trapani
> 
> Maître de Conférences
> 
> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1]
> 
> -
> 
> Centre de Biologie Structurale (CBS)
> 
> 29 rue de Navacelles
> 
> 34090 MONTPELLIER Cedex, France
> 
> Tel : +33 (0)4 67 41 77 29
> 
> Fax : +33 (0)4 67 41 79 13
> 
> -
> 
> Université de Montpellier
> 
> CNRS UMR 5048
> 
> INSERM UMR 1054
> 
> -
> 
> -- 
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Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

[Stuart McNicholas]

Dear Stefano,
  It might be possible to do what you want in a roundabout way:

i) Apply matrix to molecule: Molecule Icon -> Transform coordinates ->
Enter transformation
ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file.
iii) Load in the saved molecule
iv) For the new file: Molecule Icon -> Create crystal object.

(Maybe ii) and iii) are not necessary.)

Best wishes,
Stuart

On Wed, 2 Jun 2021 at 13:50, Stefano Trapani  wrote:
>
> Dear all
>
> I would like to visually compare (using some molecular graphics software) the 
> crystal packing of two different crystal forms of the same protein.
>
> In order to identify the similarities/differences between the crystal 
> packings, I need to change the default unit cell origin and orientation of 
> one of the crystal forms.
>
> Is there a way, in CCP4MG or other molecular graphics software, to apply a 
> given rotation/translation matrix to a "crystal object" (not to a single 
> molecular object), so that further expansions of the object by  crystal 
> symmetry will be consistent with the new origin/orientation ?
>
> If yes: can the transformation be defined by a least-squares superposition 
> between molecules from the two crystal objects ?
>
> Best regards
>
> --
> Stefano Trapani
>
> Maître de Conférences
> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
> -
> Centre de Biologie Structurale (CBS)
> 29 rue de Navacelles
> 34090 MONTPELLIER Cedex, France
>
> Tel : +33 (0)4 67 41 77 29
> Fax : +33 (0)4 67 41 79 13
> -
> Université de Montpellier
> CNRS UMR 5048
> INSERM UMR 1054
> -
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> 
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> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] {Disarmed} AW: [ccp4bb] superpose crystal objects in CCP4MG or other software

[Stuart McNicholas]

Does "Contents one unit cell", then "Extend unit cell" do this?

Stuart

On Wed, 2 Jun 2021 at 14:14, Stefano Trapani  wrote:
>
> Yes, that is the way I usually do, but it can be cumbersome.
>
> It would be easier if I could first superpose two molecules from the two 
> crystals, and then decide in which directions to expand by crystal symmetry 
> (I want to compare layers and rows of molecules).
>
> Best regards
>
> Stefano
>
> Le 2021-06-02 15:05, Schreuder, Herman /DE a écrit :
>
> Dear Stefano,
>
> I do not know if it is possible, but as a workaround, you could first expand 
> your object by crystallographic symmetry and then do the superposition.
>
> Best,
>
> Herman
>
>
>
> Von: CCP4 bulletin board  Im Auftrag von Stefano 
> Trapani
> Gesendet: Mittwoch, 2. Juni 2021 14:31
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [ccp4bb] superpose crystal objects in CCP4MG or other software
>
>
>
> Dear all
>
> I would like to visually compare (using some molecular graphics software) the 
> crystal packing of two different crystal forms of the same protein.
>
> In order to identify the similarities/differences between the crystal 
> packings, I need to change the default unit cell origin and orientation of 
> one of the crystal forms.
>
> Is there a way, in CCP4MG or other molecular graphics software, to apply a 
> given rotation/translation matrix to a "crystal object" (not to a single 
> molecular object), so that further expansions of the object by  crystal 
> symmetry will be consistent with the new origin/orientation ?
>
> If yes: can the transformation be defined by a least-squares superposition 
> between molecules from the two crystal objects ?
>
> Best regards
>
> --
> Stefano Trapani
>
>
>
> Maître de Conférences
>
> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani
>
> -
>
> Centre de Biologie Structurale (CBS)
>
> 29 rue de Navacelles
>
> 34090 MONTPELLIER Cedex, France
>
>
>
> Tel : +33 (0)4 67 41 77 29
>
> Fax : +33 (0)4 67 41 79 13
>
> -
>
> Université de Montpellier
>
> CNRS UMR 5048
>
> INSERM UMR 1054
>
> -
>
>
> --
> This message has been scanned for viruses and
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>
>
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Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

[Stefano Trapani]

 

Dear Stuart 

That does not work. 

"Transform coordinates" seems to move molecules, but not the crystal
symmetry elements (no update of the crystal symmetry operation
matrices), so that crystal symmetry expansion after "Transform
coordinates" does not generate a rotated/translated version of the
"whole" crystal, but a new (different) crystal packing. 

Stefano 

Le 2021-06-02 15:14, Stuart McNicholas a écrit : 

> Dear Stefano,
> It might be possible to do what you want in a roundabout way:
> 
> i) Apply matrix to molecule: Molecule Icon -> Transform coordinates ->
> Enter transformation
> ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file.
> iii) Load in the saved molecule
> iv) For the new file: Molecule Icon -> Create crystal object.
> 
> (Maybe ii) and iii) are not necessary.)
> 
> Best wishes,
> Stuart
> 
> On Wed, 2 Jun 2021 at 13:50, Stefano Trapani  wrote:
> 
>> Dear all I would like to visually compare (using some molecular graphics 
>> software) the crystal packing of two different crystal forms of the same 
>> protein. In order to identify the similarities/differences between the 
>> crystal packings, I need to change the default unit cell origin and 
>> orientation of one of the crystal forms. Is there a way, in CCP4MG or other 
>> molecular graphics software, to apply a given rotation/translation matrix to 
>> a "crystal object" (not to a single molecular object), so that further 
>> expansions of the object by crystal symmetry will be consistent with the new 
>> origin/orientation ? If yes: can the transformation be defined by a 
>> least-squares superposition between molecules from the two crystal objects ? 
>> Best regards -- Stefano Trapani Maître de Conférences 
>> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1] 
>> - Centre de Biologie Structurale (CBS) 
>> 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel :
+33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 
- Université de Montpellier CNRS UMR 5048 
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Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

[Boaz Shaanan]

Hi Stefano,
Did you try first to expand a unit cell in each lattice (using its symmops) and 
then superimpose two molecules from each lattice? Perhaps the expanded lattice 
wil move with the moving molecule?
I don't know how to do this in ccp4mg but I think it's possible in Chimera.

My 2p.
Cheers,
Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel

On Jun 2, 2021 16:59, Stefano Trapani  wrote:

Dear Stuart

That does not work.

"Transform coordinates" seems to move molecules, but not the crystal symmetry 
elements (no update of the crystal symmetry operation matrices), so that 
crystal symmetry expansion after "Transform coordinates" does not generate a 
rotated/translated version of the "whole" crystal, but a new (different) 
crystal packing.

Stefano

Le 2021-06-02 15:14, Stuart McNicholas a écrit :

Dear Stefano,
  It might be possible to do what you want in a roundabout way:

i) Apply matrix to molecule: Molecule Icon -> Transform coordinates ->
Enter transformation
ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file.
iii) Load in the saved molecule
iv) For the new file: Molecule Icon -> Create crystal object.

(Maybe ii) and iii) are not necessary.)

Best wishes,
Stuart

On Wed, 2 Jun 2021 at 13:50, Stefano Trapani 
mailto:trap...@cbs.cnrs.fr>> wrote:

Dear all I would like to visually compare (using some molecular graphics 
software) the crystal packing of two different crystal forms of the same 
protein. In order to identify the similarities/differences between the crystal 
packings, I need to change the default unit cell origin and orientation of one 
of the crystal forms. Is there a way, in CCP4MG or other molecular graphics 
software, to apply a given rotation/translation matrix to a "crystal object" 
(not to a single molecular object), so that further expansions of the object by 
crystal symmetry will be consistent with the new origin/orientation ? If yes: 
can the transformation be defined by a least-squares superposition between 
molecules from the two crystal objects ? Best regards -- Stefano Trapani Maître 
de Conférences 
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani 
- Centre de Biologie Structurale (CBS) 29 
rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 
Fax : +33 (0)4 67 41 79 13 - Université de 
Montpellier CNRS UMR 5048 INSERM UMR 1054 - 
-- This message has been scanned for viruses and dangerous content by 
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On Jun 2, 2021 16:59, Stefano Trapani  wrote:

Dear Stuart

That does not work.

"Transform coordinates" seems to move molecules, but not the crystal symmetry 
elements (no update of the crystal symmetry operation matrices), so that 
crystal symmetry expansion after "Transform coordinates" does not generate a 
rotated/translated version of the "whole" crystal, but a new (different) 
crystal packing.

Stefano

Le 2021-06-02 15:14, Stuart McNicholas a écrit :

Dear Stefano,
  It might be possible to do what you want in a roundabout way:

i) Apply matrix to molecule: Molecule Icon -> Transform coordinates ->
Enter transformation
ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file.
iii) Load in the saved molecule
iv) For the new file: Molecule Icon -> Create crystal object.

(Maybe ii) and iii) are not necessary.)

Best wishes,
Stuart

On Wed, 2 Jun 2021 at 13:50, Stefano Trapani 
mailto:trap...@cbs.cnrs.fr>> wrote:

Dear all I would like to visually compare (using some molecular graphics 
software) the crystal packing of two different crystal forms of the same 
protein. In order to identify the similarities/differences between the crystal 
packings, I need to change the default unit cell origin and orientation of one 
of the crystal forms. Is there a way, in CCP4MG or other molecular graphics 
software, to apply a given rotation/translation matrix to a "crystal object" 
(not to a single molecular object), so that further expansions of the object by 
crystal symmetry will be consistent with the new origin/orientation ? If yes: 
can the transformation be defined by a least-squares superposition between 
molecules from the two crystal objects ? Best regards -- Stefano Trapani Maître 
de Conférences 
http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani 
- Centre de Biologie Structurale (CBS) 29

Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

[Stefano Trapani]

 

Hi Boaz 

Thank you. 

That works in Chimera (first superpose, then symmetry expand) but not in
CCP4MG (independently of the order of the operations). 

It would be nice to have an equivalent option implemented in CCP4MG. 

Best regards 

Stefano Trapani 

Le 2021-06-02 16:20, Boaz Shaanan a écrit : 

> Hi Stefano, 
> Did you try first to expand a unit cell in each lattice (using its symmops) 
> and then superimpose two molecules from each lattice? Perhaps the expanded 
> lattice wil move with the moving molecule? 
> I don't know how to do this in ccp4mg but I think it's possible in Chimera. 
> 
> My 2p. 
> Cheers, 
> Boaz
> 
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben Gurion University
> Beer Sheva, Israel 
> 
> On Jun 2, 2021 16:59, Stefano Trapani  wrote:
> 
> Dear Stuart 
> 
> That does not work. 
> 
> "Transform coordinates" seems to move molecules, but not the crystal symmetry 
> elements (no update of the crystal symmetry operation matrices), so that 
> crystal symmetry expansion after "Transform coordinates" does not generate a 
> rotated/translated version of the "whole" crystal, but a new (different) 
> crystal packing. 
> 
> Stefano 
> 
> Le 2021-06-02 15:14, Stuart McNicholas a écrit : 
> 
> Dear Stefano,
> It might be possible to do what you want in a roundabout way:
> 
> i) Apply matrix to molecule: Molecule Icon -> Transform coordinates ->
> Enter transformation
> ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file.
> iii) Load in the saved molecule
> iv) For the new file: Molecule Icon -> Create crystal object.
> 
> (Maybe ii) and iii) are not necessary.)
> 
> Best wishes,
> Stuart
> 
> On Wed, 2 Jun 2021 at 13:50, Stefano Trapani  wrote:
> Dear all I would like to visually compare (using some molecular graphics 
> software) the crystal packing of two different crystal forms of the same 
> protein. In order to identify the similarities/differences between the 
> crystal packings, I need to change the default unit cell origin and 
> orientation of one of the crystal forms. Is there a way, in CCP4MG or other 
> molecular graphics software, to apply a given rotation/translation matrix to 
> a "crystal object" (not to a single molecular object), so that further 
> expansions of the object by crystal symmetry will be consistent with the new 
> origin/orientation ? If yes: can the transformation be defined by a 
> least-squares superposition between molecules from the two crystal objects ? 
> Best regards -- Stefano Trapani Maître de Conférences 
> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani [1] 
> - Centre de Biologie Structurale (CBS) 29 
> rue de Navacelles 34090 MONTPELLIER Cedex, France Tel :
+33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 
- Université de Montpellier CNRS UMR 5048 
INSERM UMR 1054 - -- This message has been 
scanned for viruses and dangerous content by MailScanner, and is believed to be 
clean.  To unsubscribe from the CCP4BB list, 
click the following link: 
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On Jun 2, 2021 16:59, Stefano Trapani  wrote:

> Dear Stuart 
> 
> That does not work. 
> 
> "Transform coordinates" seems to move molecules, but not the crystal symmetry 
> elements (no update of the crystal symmetry operation matrices), so that 
> crystal symmetry expansion after "Transform coordinates" does not generate a 
> rotated/translated version of the "whole" crystal, but a new (different) 
> crystal packing. 
> 
> Stefano 
> 
> Le 2021-06-02 15:14, Stuart McNicholas a écrit : 
> 
> Dear Stefano,
> It might be possible to do what you want in a roundabout way:
> 
> i) Apply matrix to molecule: Molecule Icon -> Transform coordinates ->
> Enter transformation
> ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file.
> iii) Load in the saved molecule
> iv) For the new file: Molecule Icon -> Create crystal object.
> 
> (Maybe ii) and iii) are not necessary.)
> 
> Best wishes,
> Stuart
> 
> On Wed, 2 Jun 2021 at 13:50, Stefano Trapani  wrote:
> Dear all I would like to visually compare (using some molecular graphics 
> software) the crystal packing of two different crystal forms of the same 
> protein. In order to identify the similarities/differences between the 
> crystal packings, I need to change the default unit cell origin and 
> orientation of one of the crystal forms. Is there a way, in CCP4MG or other 
> molecular graphics software, to apply a given rotation/translation matrix to 
> a "crystal object" (not to a single molecular object), so tha

[ccp4bb] PhD position in Structural Biology, University of Exeter/Dstl

[Harmer, Nicholas]

Dear all,

My group at the Living Systems Institute in Exeter is seeking to appoint a PhD 
position on a four year studentship. This is an industrial partnership award 
with Dstl (UK). Unfortunately because of the conditions of the funding we can 
only consider UK nationals.

The position will be using structural and biochemical methods to characterise 
potential drug targets from the biosecurity pathogen Coxiella burnetii. We will 
use X-ray crystallography and single particle cryo-EM as necessary to solve the 
scientific challenges. The student appointed will have the opportunity to work 
with Dstl and experts in complementary techniques at the Living Systems 
Institute.

The deadline for applications is 15th June, and I am very happy to answer any 
queries from interested students. Full details and the applications portal are 
available at https://www.swbio.ac.uk/case-studentships-2/.

Thanks,

Nicholas Harmer



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[ccp4bb] Consistent Format for Validation and Coordinate Data in the PDB archive

[Jasmine Young]

wwPDB validation reports are now provided in PDBx/mmCIF format for all 
new depositions in OneDep. This change makes validation data more 
interoperable with the PDB archival format. Data are more logically and 
better organized in the PDBx/mmCIF reports, and therefore more 
“database-friendly” than the report in XML format. PDBx/mmCIF-format 
validation reports for newly released and modified entries will be 
distributed through the PDB 
 and EMDB 
 Core Archives.


The new PDBx/mmCIF reports are easier to interpret. They contain a 
high-level summary and offer easier access to residue-level information. 
Data are provided at multiple levels: entity, chain-specific, and even 
at the individual residues. For example, it is more straightforward to 
obtain the total number of clashes. The corresponding validation 
dictionary is available at 
mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Index 
. 
Examples of PDBx/mmCIF validation reports for X-ray, 3DEM, and NMR are 
publicly available at GitHub 
.


PDBx/mmCIF validation reports will be provided for the full PDB and EMDB 
archives once archival validation recalculation is performed.


wwPDB strongly recommends all PDB users and software developers adopt 
this format for future applications.



--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




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[ccp4bb] Multiple positions for postdoctoral Fellow National Cancer Institute, Maryland

[Lea, Susan (NIH/NCI) [E]]

Dear All,

I am recruiting up to six fellows for my new lab at the NCI, Frederick. 
Projects will range from eukaryotic transporters and receptors to bacterial 
nano machines. Please get in touch if you are interested! See advertisement 
below.

All the best
Susan

Chief of the Center for Structural Biology
National Cancer Institute
Frederick
Maryland
USA

Department of Health and Human Services (DHHS)
National Institutes of Health (NIH)
National Cancer Institute (NCI)
Center for Cancer Research (CCR)

Five postdoctoral positions are available in The Molecular Basis of Disease 
Section (MBDS), Center for Structural Biology (CSB), Center for Cancer Research 
(CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), 
Department of Health and Human Services (DHHS), Frederick, MD.  The candidate 
will perform basic research in molecular biology/structural 
biology/biochemistry.

The MBDS group uses mixed structural methods to study host-pathogen 
interactions and other medically important molecular pathways with a particular 
focus on membrane resident protein complexes. We use and develop cutting-edge 
structural methods including cryo-electron microscopy and X-ray crystallography 
to define molecular mechanisms involved in health and disease states.

The research of the group is supported by the collaborative and 
interdisciplinary NIH intramural program, which includes more than 1100 labs 
and provides state-of-the-art equipment in structural biology, biochemistry, 
and biophysics. These core facilities are supported by Ph.D. level staff and 
offer hands-on training. In addition, NIH is committed to the continuing 
education and career development of its research staff through numerous courses 
and workshops offered by NIH Office of Intramural Training & Education (OITE) 
and Foundation for Advanced Education in the Sciences (FAES). There are also 
opportunities for intramural career transition funding (K grants).

Interested candidates must have a Ph.D. or M.D. degree with less than 5 years 
of postdoctoral experience.  Applicants must have a strong background in 
molecular biology, structural biology,  biochemistry, or a related discipline. 
The candidate should have good oral and written skills in English. The 
candidate should be skilled in at least one of the following areas: 
Biochemistry and molecular biology (experience in protein purification from 
different expression systems of soluble and membrane proteins); Electron 
microscopy (experience in cryo-EM sample preparation and digital image 
processing). We have excellent access to high-end microscopes (Titan Krios/Cold 
FEG/Selectris / Falcon IV, Arctica/BioQuantum/K3 and Aquilos II CryoFIB 
available locally in addition to smaller testing microscopes); Crystallography 
(experience in protein crystal structure determination). We have excellent 
access to Synchrotron beamlines and in-house X-ray diffraction and SAXS cores.

The candidate must be highly motivated to participate in rigorous and 
innovative research programs and possess excellent work ethic and team spirit, 
be able to work independently and efficiently and collaborate closely with 
members of the group, and other labs on joint projects.

The research group is supported by the collaborative and interdisciplinary NIH 
intramural and offers competitive salary and comprehensive health insurance.  
Appointments will be one year initially and renewable up to a total of 3-5 
years based on performance.  The NIH is dedicated to building a diverse 
community in its training and employment programs.  This position is subject to 
a background investigation.

Interested applicants should send a cover letter indicating preferred starting 
date, a brief description (1-2 pages) of past research, CV, and contact 
information for at least three references via email to Susan Lea D.Phil.: 
lealabrecr...@nih.gov). More information about 
MBDS can be found at: 
https://ccr.cancer.gov/center-for-structural-biology/susan-m-lea. The Center 
for Structural Biology is located on the Frederick campus of NCI in Frederick, 
Maryland, USA. Frederick was founded in 1745 and is a city of ~70,000 
inhabitants, 45 minutes from the central NIH, Bethesda Campus. Surrounded by 
State Parks, you can ski within 30 minutes of the campus in the winter and 
enjoy the many wineries, breweries and other thriving, independent, hostelries 
in the summer.

DHHS, NIH, and NCI are Equal Opportunity Employers

Recent Related Papers from Group:
Parker, J.L.^, Deme, J.C.^, Kuteyi, G., Wu, Z., Huo, J., Goldman, I.D., Owens, 
R., Biggin, P.C., Lea, S.M.* & Newstead, S.* (2021) “Structural basis for 
antifolate transport by the proton-coupled folate transporter PCFT” Nature 
https://doi.org/10.1038/s41586-021-03579-z
Johnson, S.^*, Furlong, E.J.^, Deme, J.C., Nord, A.L., Caesar, J.C., Chevance, 
F.V., Berry, R.M., Hughes, K.T. & Lea, S.M.* (2021) “Molecular structure of the 
intact bacteri

Re: [ccp4bb] Meaning of a pdb entry

[Marcin Wojdyr]

Dear Gergely,

>
> Thank you for these examples! It is reassuring to see that multiple 
> crystallographic models do not break validation for example. I assume only 
> the validation of the first model and first reflection file is shown. I can 
> imagine that it is still a substantial change and may require an extended 
> description to make such depositions fully functional. I will ask the PDB, 
> but this made me optimistic. It would be easy to implement Tim's method if it 
> works for deposition.

I think it won't work.

(1) One entry can contain an ensemble of many models. 4PTH has 250
models and each atom has occupancy 0.004. It's similar to alternative
locations, but taken to extremes.

(2) One entry can contain a single model and multiple datasets. 5RKZ
has 1500+ datasets from crystals soaked with different compounds. You
can concatenate reflection mmCIF files, but only the first block is
used for validation. I suppose all the models were similar, so one can
obtain them by refining the single deposited model to each dataset.

I don't think you can meaningfully deposit multiple datasets with
corresponding models in a single entry. (2) is probably the closest to
what you want.

Best wishes,
Marcin



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Re: [ccp4bb] superpose crystal objects in CCP4MG or other software

[Jon Cooper]

I am thinking this could be done using pdbset to apply symops and origin 
shifts, etc, with a bit of checking in Coot, creative chain-ID's and some trial 
and error? Or using Coot to apply symops and save the resulting pdb's with 
different chain ID's and then concatenate them into a mini-lattice? Cheers, 
Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 2 Jun 2021, 15:42, Stefano Trapani wrote:

> Hi Boaz
>
> Thank you.
>
> That works in Chimera (first superpose, then symmetry expand) but not in 
> CCP4MG (independently of the order of the operations).
>
> It would be nice to have an equivalent option implemented in CCP4MG.
>
> Best regards
>
> Stefano Trapani
>
> Le 2021-06-02 16:20, Boaz Shaanan a écrit :
>
>> Hi Stefano,
>> Did you try first to expand a unit cell in each lattice (using its symmops) 
>> and then superimpose two molecules from each lattice? Perhaps the expanded 
>> lattice wil move with the moving molecule?
>> I don't know how to do this in ccp4mg but I think it's possible in Chimera.
>>
>> My 2p.
>> Cheers,
>> Boaz
>>
>> Boaz Shaanan, Ph.D.
>> Dept. of Life Sciences
>> Ben Gurion University
>> Beer Sheva, Israel
>>
>> On Jun 2, 2021 16:59, Stefano Trapani  wrote:
>>
>>> Dear Stuart
>>>
>>> That does not work.
>>>
>>> "Transform coordinates" seems to move molecules, but not the crystal 
>>> symmetry elements (no update of the crystal symmetry operation matrices), 
>>> so that crystal symmetry expansion after "Transform coordinates" does not 
>>> generate a rotated/translated version of the "whole" crystal, but a new 
>>> (different) crystal packing.
>>>
>>> Stefano
>>>
>>> Le 2021-06-02 15:14, Stuart McNicholas a écrit :
>>>
 Dear Stefano,
   It might be possible to do what you want in a roundabout way:

 i) Apply matrix to molecule: Molecule Icon -> Transform coordinates ->
 Enter transformation
 ii) Save the molecule: Molecule Icon -> File save/restore -> Save to file.
 iii) Load in the saved molecule
 iv) For the new file: Molecule Icon -> Create crystal object.

 (Maybe ii) and iii) are not necessary.)

 Best wishes,
 Stuart

 On Wed, 2 Jun 2021 at 13:50, Stefano Trapani <
 trap...@cbs.cnrs.fr
> wrote:

> Dear all I would like to visually compare (using some molecular graphics 
> software) the crystal packing of two different crystal forms of the same 
> protein. In order to identify the similarities/differences between the 
> crystal packings, I need to change the default unit cell origin and 
> orientation of one of the crystal forms. Is there a way, in CCP4MG or 
> other molecular graphics software, to apply a given rotation/translation 
> matrix to a "crystal object" (not to a single molecular object), so that 
> further expansions of the object by crystal symmetry will be consistent 
> with the new origin/orientation ? If yes: can the transformation be 
> defined by a least-squares superposition between molecules from the two 
> crystal objects ? Best regards -- Stefano Trapani Maître de Conférences 
> http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani 
> - Centre de Biologie Structurale 
> (CBS) 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 
> 67 41 77 29 Fax : +33 (0)4 67 41 79 13 
> - Université de Montpellier CNRS UMR 
> 5048 INSERM UMR 1054 - -- This 
> message has been scanned for viruses and dangerous content by 
> MailScanner, and is believed to be clean. 
>  To unsubscribe from the CCP4BB list, 
> click the following link: 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by [MailScanner](http://www.mailscanner.info/), and is
>>> believed to be clean.
>>>
>>> ---
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> On Jun 2, 2021 16:59, Stefano Trapani  wrote:
>>
>>> Dear Stuart
>>>
>>> That does not work.
>>>
>>> "Transform coordinates" seems to move molecules, but not the crystal 
>>> symmetry elements (no update of the crystal symmetry operation matrices), 
>>> so that crystal symmetry expansion after "Transform coordinates" does not 
>>> generate a rotated/translated version of the "whole" crystal, but a new 
>>> (different) crystal packing.
>>>
>>> Stefano
>>>
>>> Le 2021-06-02 15:14, Stuart McNicholas a écrit :
>>>
 Dear Stefano,
   It might be possible to do what you want in a roundabout way:

 i) Apply matrix to molecule: Molecule Icon -> Transform coordinates ->
 Enter transformation
 ii) Save the molecule: Molecule Icon -> File